Offline Level-1 Assembly

Use case

You have an abstract level-1 SBOL design and local SBOL collections containing the required part plasmids, backbone plasmids, and enzyme implementations. You want BuildCompiler to produce:

• an assembled product SBOL document,

• a deterministic PUDU assembly input JSON file, and

• a list of route inputs used to build the plasmid.

Example

from pathlib import Path

import sbol2

from buildcompiler.abstract_translator import extract_toplevel_definition
from buildcompiler.adapters.pudu import write_assembly_pudu_input_json
from buildcompiler.buildcompiler import BuildCompiler

test_files = Path("tests/test_files")
collection_docs = []
for filename in (
    "CIDARMoCloParts_collection.xml",
    "CIDARMoCloPlasmidsKit_collection.xml",
    "Enzyme_Implementations_collection.xml",
    "impl_test_collection.xml",
):
    doc = sbol2.Document()
    doc.read(str(test_files / filename))
    collection_docs.append(doc)

design_doc = sbol2.Document()
design_doc.read(str(test_files / "abstract_design.xml"))
design = extract_toplevel_definition(design_doc)

compiler = BuildCompiler.from_local_documents(
    collection_docs,
    design_doc=design_doc,
)

product_doc = sbol2.Document()
routes, product_doc = compiler.assembly_lvl1(
    [design],
    final_doc=product_doc,
    product_name="offline_lvl1",
)

results = Path("results/offline_lvl1")
results.mkdir(parents=True, exist_ok=True)
(results / "offline_lvl1_products.xml").write_text(
    product_doc.writeString(),
    encoding="utf-8",
)
write_assembly_pudu_input_json(
    compiler.last_assembly_pudu_json,
    results / "offline_lvl1_pudu_input.json",
)

The generated PUDU input has this shape:

[
  {
    "Product": "http://buildcompiler.org/offline_lvl1/1",
    "Backbone": "https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVK_AE/1",
    "PartsList": [
      "https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23100_AB/1",
      "https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0034_BC/1",
      "https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pE0040_CD/1",
      "https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0015_DE/1"
    ],
    "Restriction Enzyme": "https://synbiohub.org/user/Gon/Enzyme_Implementations/BsaI/1"
  }
]

Notes

compiler.last_assembly_pudu_json is populated by the assembly stage from the route selected by BuildCompiler. It does not scrape the generated SBOL document, so it retains the product plasmid, backbone plasmid, part plasmids, and enzyme implementation used by the route.